beta: opensim integration

2024-09-19 00:39:58 +02:00 · 2024-09-19 00:39:58 +02:00 · e321228a75
commit e321228a75
parent 6bb2c3fd9c
7 changed files with 106 additions and 68 deletions
--- a/Content/Pose2Sim_workflow.jpg
+++ b/Content/Pose2Sim_workflow.jpg
--- a/Pose2Sim/Pose2Sim.py
+++ b/Pose2Sim/Pose2Sim.py
@ -39,7 +39,7 @@ Pose2Sim.personAssociation()
 Pose2Sim.triangulation()
 Pose2Sim.filtering()
 Pose2Sim.markerAugmentation()
-Pose2Sim.opensimProcessing()
+Pose2Sim.kinematics()
 # Then run OpenSim (see Readme.md)
 '''

@ -158,7 +158,6 @@ def read_config_files(config):
    return level, config_dicts


-
 def calibration(config=None):
    '''
    Cameras calibration from checkerboards or from qualisys files.
@ -192,7 +191,11 @@ def calibration(config=None):
    logging.info("---------------------------------------------------------------------\n")
    start = time.time()

-    calibrate_cams_all(config_dict)
+    try:
+        calibrate_cams_all(config_dict)
+    except Exception as e:
+        logging.error(f"Error during calibration: {e}")
+        return

    end = time.time()
    logging.info(f'\nCalibration took {end-start:.2f} s.\n')
@ -236,7 +239,11 @@ def poseEstimation(config=None):
        logging.info(f"Project directory: {project_dir}")
        logging.info("---------------------------------------------------------------------\n")

-        rtm_estimator(config_dict)
+        try:
+            rtm_estimator(config_dict)
+        except Exception as e:
+            logging.error(f"Error during pose estimation: {e}")
+            continue

        end = time.time()
        elapsed = end - start
@ -280,7 +287,11 @@ def synchronization(config=None):
        logging.info(f"Project directory: {project_dir}")
        logging.info("---------------------------------------------------------------------\n")

-        synchronize_cams_all(config_dict)
+        try:
+            synchronize_cams_all(config_dict)
+        except Exception as e:
+            logging.error(f"Error during synchronization: {e}")
+            continue

        end = time.time()
        elapsed = end-start
@ -327,7 +338,11 @@ def personAssociation(config=None):
        logging.info(f"Project directory: {project_dir}")
        logging.info("---------------------------------------------------------------------\n")

-        track_2d_all(config_dict)
+        try:
+            track_2d_all(config_dict)
+        except Exception as e:
+            logging.error(f"Error during person association: {e}")
+            continue

        end = time.time()
        elapsed = end-start
@ -373,7 +388,11 @@ def triangulation(config=None):
        logging.info(f"Project directory: {project_dir}")
        logging.info("---------------------------------------------------------------------\n")

-        triangulate_all(config_dict)
+        try:
+            triangulate_all(config_dict)
+        except Exception as e:
+            logging.error(f"Error during triangulation: {e}")
+            continue

        end = time.time()
        elapsed = end-start
@ -418,7 +437,11 @@ def filtering(config=None):
        logging.info(f"Project directory: {project_dir}\n")
        logging.info("---------------------------------------------------------------------\n")

-        filter_all(config_dict)
+        try:
+            filter_all(config_dict)
+        except Exception as e:
+            logging.error(f"Error during filtering: {e}")
+            continue

        logging.info('\n')

@ -459,31 +482,32 @@ def markerAugmentation(config=None):
        logging.info(f"Project directory: {project_dir}")
        logging.info("---------------------------------------------------------------------\n")

-        augmentTRC(config_dict)
+        try:
+            augmentTRC(config_dict)
+        except Exception as e:
+            logging.error(f"Error during marker augmentation: {e}")
+            continue

        end = time.time()
        elapsed = end-start
        logging.info(f'\nMarker augmentation took {time.strftime("%Hh%Mm%Ss", time.gmtime(elapsed))}.\n')


-def opensimProcessing(config=None):
+def kinematics(config=None):
    '''
    Performing OpenSim scaling and inverse kinematics.
-    Selected the 10% slowest frames from trc for scaling
-    Saved as .osim and .mot
+    Select the 10% slowest frames from trc for scaling
+    Save scaled model as .osim and output motion as .mot

    config can be a dictionary,
    or a the directory path of a trial, participant, or session,
    or the function can be called without an argument, in which case it the config directory is the current one.
    '''

-    from Pose2Sim.kinematics import opensimProcessing
-
-    # Read the configuration files
+    from Pose2Sim.kinematics import kinematics
    level, config_dicts = read_config_files(config)

-    # Ensure the configuration is properly structured
-    if isinstance(config, dict):
+    if type(config) == dict:
        config_dict = config_dicts[0]
        if config_dict.get('project').get('project_dir') is None:
            raise ValueError('Please specify the project directory in config_dict:\n \
@ -502,24 +526,23 @@ def opensimProcessing(config=None):
        frames = ["all frames" if frame_range == [] else f"frames {frame_range[0]} to {frame_range[1]}"][0]

        logging.info("\n---------------------------------------------------------------------")
-        logging.info(f"OpenSim processing for {seq_name}, for {frames}.")
+        logging.info(f"OpenSim scaling and inverse kinematics for {seq_name}, for {frames}.")
        logging.info(f"On {currentDateAndTime.strftime('%A %d. %B %Y, %H:%M:%S')}")
        logging.info(f"Project directory: {project_dir}")
        logging.info("---------------------------------------------------------------------\n")

        try:
-            opensimProcessing(config_dict)
-
+            kinematics(config_dict)
        except Exception as e:
            logging.error(f"Error during OpenSim processing: {e}")
            continue

        end = time.time()
        elapsed = end - start
-        logging.info(f'\nOpenSim processing took {time.strftime("%Hh%Mm%Ss", time.gmtime(elapsed))}.\n')
+        logging.info(f'\nOpenSim scaling and inverse kinematics took {time.strftime("%Hh%Mm%Ss", time.gmtime(elapsed))}.\n')


-def runAll(config=None, do_calibration=True, do_poseEstimation=True, do_synchronization=True, do_personAssociation=True, do_triangulation=True, do_filtering=True, do_markerAugmentation=True, do_opensimProcessing=True):
+def runAll(config=None, do_calibration=True, do_poseEstimation=True, do_synchronization=True, do_personAssociation=True, do_triangulation=True, do_filtering=True, do_markerAugmentation=True, do_kinematics=True):
    '''
    Run all functions at once. Beware that Synchronization, personAssociation, and markerAugmentation are not always necessary,
    and may even lead to worse results. Think carefully before running all.
@ -610,11 +633,11 @@ def runAll(config=None, do_calibration=True, do_poseEstimation=True, do_synchron
        logging.info('Skipping marker augmentation.')
        logging.info("\n\n=====================================================================")

-    if do_opensimProcessing:
+    if do_kinematics:
        logging.info("\n\n=====================================================================")
        logging.info("Running OpenSim processing.")
        logging.info("=====================================================================")
-        opensimProcessing(config)
+        kinematics(config)
    else:
        logging.info("\n\n=====================================================================")
        logging.info('Skipping OpenSim processing.')
--- a/Pose2Sim/Utilities/calib_qca_to_toml.py
+++ b/Pose2Sim/Utilities/calib_qca_to_toml.py
@ -39,9 +39,9 @@ __status__ = "Development"

 ## FUNCTIONS
 def natural_sort_key(s):
-    """
+    '''
    Key for natural sorting of strings containing numbers.
-    """
+    '''
    return [int(c) if c.isdigit() else c.lower() for c in re.split(r'(\d+)', s)]


--- a/Pose2Sim/Utilities/tests.py
+++ b/Pose2Sim/Utilities/tests.py
@ -7,31 +7,49 @@
    ## Pose2Sim tests                     ##
    ########################################
    
-    - BATCH SESSION:
-        - Calibration conversion from .qca.txt
-        - Single person:
-            - synchronization
-            - person association
-            - triangulation
-            - filtering
-            - marker augmentation
-            - opensim processing
-        - Multi-person:
-            - synchronization
-            - person association
-            - triangulation
-            - filtering
-            - marker augmentation
-            - opensim processing
-            
-    - SINGLE TRIAL:
-        - calibration
+    - SINGLE PERSON:
+        - calibration conversion from .qca.txt
+        - pose estimation
        - synchronization
        - person association
        - triangulation
        - filtering
        - marker augmentation
-        - opensim processing
+        - opensim scaling and inverse kinematics
+        
+        - run all
+
+    - MULTI PERSON:
+        - calibration conversion from .qca.txt
+        - pose estimation
+        - NO synchronization
+        - person association
+        - triangulation
+        - filtering
+        - marker augmentation
+        - opensim scaling and inverse kinematics
+
+        - run all
+
+    - BATCH SESSION, RUN ALL:
+        - Calibration conversion from .qca.txt
+        - Single person:
+            - pose estimation
+            - NO synchronization
+            - person association
+            - triangulation
+            - filtering
+            - marker augmentation
+            - opensim scaling and inverse kinematics
+        - Multi-person:
+            - pose estimation
+            - NO synchronization
+            - person association
+            - triangulation
+            - filtering
+            - marker augmentation
+            - opensim scaling and inverse kinematics
+            

    N.B.: 
    1. Calibration from scene dimensions is not tested, as it requires the 
@ -77,13 +95,12 @@ class TestWorkflow(unittest.TestCase):
            - triangulation
            - filtering
            - marker augmentation
-            - OpenSim processing
+            - opensim scaling and inverse kinematics
            - run all

        N.B.: Calibration from scene dimensions is not tested, as it requires the 
        user to click points on the image. 
        Not all possible configuration parameters are extensively tested.
-        Scaling and inverse kinematics are not tested yet.
        
        Usage: 
        from Pose2Sim import tests; tests.test_workflow()
@ -103,7 +120,6 @@ class TestWorkflow(unittest.TestCase):
        config_dict.get("pose").update({"mode":'lightweight'})
        config_dict.get("pose").update({"display_detection":False})
        config_dict.get("synchronization").update({"display_sync_plots":False})
-        # config_dict['triangulation']['reorder_trc'] = False
        config_dict['filtering']['display_figures'] = False

        Pose2Sim.calibration(config_dict)
@ -113,7 +129,7 @@ class TestWorkflow(unittest.TestCase):
        Pose2Sim.triangulation(config_dict)
        Pose2Sim.filtering(config_dict)
        Pose2Sim.markerAugmentation(config_dict)
-        Pose2Sim.opensimProcessing(config_dict)
+        Pose2Sim.kinematics(config_dict)

        config_dict.get("pose").update({"overwrite_pose":False})
        Pose2Sim.runAll(config_dict)
@ -141,7 +157,7 @@ class TestWorkflow(unittest.TestCase):
        Pose2Sim.triangulation(config_dict)
        Pose2Sim.filtering(config_dict)
        Pose2Sim.markerAugmentation(config_dict)
-        Pose2Sim.opensimProcessing(config_dict)
+        Pose2Sim.kinematics(config_dict)

        # Run all
        config_dict.get("pose").update({"overwrite_pose":False})
--- a/Pose2Sim/markerAugmentation.py
+++ b/Pose2Sim/markerAugmentation.py
@ -36,7 +36,7 @@ from Pose2Sim.common import convert_to_c3d, natural_sort_key
 ## AUTHORSHIP INFORMATION
 __author__ = "Antoine Falisse, adapted by HunMin Kim and David Pagnon"
 __copyright__ = "Copyright 2022, OpenCap"
-__credits__ = ["Antoine Falisse", "HunMin Kim"]
+__credits__ = ["Antoine Falisse", "HunMin Kim", "David Pagnon"]
 __license__ = "Apache-2.0 License"
 __version__ = "0.9.4"
 __maintainer__ = "David Pagnon"
--- a/Pose2Sim/triangulation.py
+++ b/Pose2Sim/triangulation.py
@ -735,7 +735,6 @@ def triangulate_all(config_dict):
    multi_person = config_dict.get('project').get('multi_person')
    pose_model = config_dict.get('pose').get('pose_model')
    frame_range = config_dict.get('project').get('frame_range')
-    reorder_trc = config_dict.get('triangulation').get('reorder_trc')
    likelihood_threshold = config_dict.get('triangulation').get('likelihood_threshold_triangulation')
    interpolation_kind = config_dict.get('triangulation').get('interpolation')
    interp_gap_smaller_than = config_dict.get('triangulation').get('interp_if_gap_smaller_than')
@ -977,21 +976,21 @@ def triangulate_all(config_dict):
    if make_c3d:
        c3d_paths = [convert_to_c3d(t) for t in trc_paths]
        
-    # Reorder TRC files
-    if multi_person and reorder_trc and len(trc_paths)>1:
-        trc_id = retrieve_right_trc_order(trc_paths)
-        [os.rename(t, t+'.old') for t in trc_paths]
-        [os.rename(t+'.old', trc_paths[i]) for i, t in zip(trc_id,trc_paths)]
-        if make_c3d:
-            [os.rename(c, c+'.old') for c in c3d_paths]
-            [os.rename(c+'.old', c3d_paths[i]) for i, c in zip(trc_id,c3d_paths)]
-        error_tot = [error_tot[i] for i in trc_id]
-        nb_cams_excluded_tot = [nb_cams_excluded_tot[i] for i in trc_id]
-        cam_excluded_count = [cam_excluded_count[i] for i in trc_id]
-        interp_frames = [interp_frames[i] for i in trc_id]
-        non_interp_frames = [non_interp_frames[i] for i in trc_id]
+    # # Reorder TRC files
+    # if multi_person and reorder_trc and len(trc_paths)>1:
+    #     trc_id = retrieve_right_trc_order(trc_paths)
+    #     [os.rename(t, t+'.old') for t in trc_paths]
+    #     [os.rename(t+'.old', trc_paths[i]) for i, t in zip(trc_id,trc_paths)]
+    #     if make_c3d:
+    #         [os.rename(c, c+'.old') for c in c3d_paths]
+    #         [os.rename(c+'.old', c3d_paths[i]) for i, c in zip(trc_id,c3d_paths)]
+    #     error_tot = [error_tot[i] for i in trc_id]
+    #     nb_cams_excluded_tot = [nb_cams_excluded_tot[i] for i in trc_id]
+    #     cam_excluded_count = [cam_excluded_count[i] for i in trc_id]
+    #     interp_frames = [interp_frames[i] for i in trc_id]
+    #     non_interp_frames = [non_interp_frames[i] for i in trc_id]
        
-        logging.info('\nThe trc and c3d files have been renamed to match the order of the static sequences.')
+    #     logging.info('\nThe trc and c3d files have been renamed to match the order of the static sequences.')


    # Recap message
--- a/setup.cfg
+++ b/setup.cfg
@ -1,6 +1,6 @@
 [metadata]
 name = pose2sim
-version = 0.9.12
+version = 0.9.13
 author = David Pagnon
 author_email = contact@david-pagnon.com
 description = Perform a markerless kinematic analysis from multiple calibrated views as a unified workflow from an OpenPose input to an OpenSim result.